Contacts of the strand formed by residues 121 - 128 (chain B) in PDB entry 1NQ3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 121 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLN 4.2 0.2 - - - +
37B LEU* 3.6 20.8 - - - +
38B GLY 4.3 1.9 + - - -
51B VAL* 4.0 14.1 - - + +
54B GLU* 3.9 14.6 - - + +
55B ALA* 3.8 30.5 - - + +
58B ALA* 5.2 2.6 - - + +
81B VAL* 4.3 5.2 - - + -
82B LEU 3.2 14.4 - - - +
83B LEU* 3.7 15.7 - - + -
92B VAL* 4.6 7.9 - - + -
115B LEU* 3.5 4.2 - - - +
119B GLY* 3.4 1.4 - - - -
120B ARG* 1.3 84.3 + - - +
122B GLU* 1.3 71.0 + - - +
123B ILE* 4.2 15.5 - - + -
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ALA* 4.2 15.6 - - - +
109A ALA 3.8 9.6 + - - +
110A TYR* 4.9 0.2 - - - -
35B GLY* 3.4 22.6 - - - +
36B GLN 3.2 20.4 - - - +
37B LEU* 3.5 15.3 - - + +
80B THR 3.8 0.9 - - - +
82B LEU* 2.9 47.6 + - + +
115B LEU* 3.6 15.8 - - + +
116B PRO* 3.4 29.6 - - - +
121B VAL* 1.3 74.1 - - - +
123B ILE* 1.3 68.4 + - - +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B SER 4.0 0.9 - - - +
35B GLY* 4.0 1.1 - - - -
36B GLN* 2.7 36.2 + - - +
55B ALA* 4.8 4.5 - - - +
58B ALA* 4.5 12.6 - - + -
59B LEU* 3.9 33.9 - - + -
62B ILE* 3.6 27.7 - - + +
79B ALA* 4.7 9.6 - - + -
80B THR 3.4 12.6 - - - +
81B VAL* 4.5 13.2 - - + -
92B VAL* 5.3 4.9 - - + -
96B TYR* 4.7 11.4 - - + -
121B VAL* 4.2 15.5 - - + -
122B GLU* 1.3 80.8 - - - +
124B GLU* 1.3 69.8 + - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LYS* 2.8 35.3 + - - -
80A THR* 4.8 3.6 + - - +
108A ALA* 3.8 17.2 - - - +
110A TYR* 4.4 8.0 + - - -
33B ILE* 4.0 9.2 - - - +
34B SER 4.4 0.9 - - - -
35B GLY* 3.8 16.8 - - - +
62B ILE* 5.1 1.1 - - - -
79B ALA* 3.2 5.2 - - - +
80B THR* 2.8 57.6 + - + +
82B LEU* 4.2 13.5 - - + +
123B ILE* 1.3 75.8 - - - +
125B ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 3.1 47.4 + - + +
62B ILE* 4.9 13.4 - - + +
76B VAL* 4.0 18.8 - - + -
78B LYS 3.1 13.7 - - - +
79B ALA* 4.1 4.5 - - + +
123B ILE* 5.4 0.2 - - + -
124B GLU* 1.3 79.9 - - - +
126B ILE* 1.3 69.6 + - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LYS* 6.0 4.9 - - - +
126A ILE* 5.7 3.4 - - + -
30B THR* 3.8 26.5 - - + -
31B ILE 3.3 5.2 - - - +
32B TYR* 4.0 26.9 - - + -
33B ILE* 5.5 0.4 - - - -
76B VAL* 3.6 4.2 - - - +
77B VAL* 3.0 33.5 + - + -
78B LYS* 2.8 27.6 + - + +
125B ALA* 1.3 80.6 - - - +
127B ALA* 1.3 62.0 + - - +
128B VAL* 5.4 0.4 - - + -
32C TYR* 3.8 32.3 - - + +
126C ILE* 5.9 2.5 - - + -
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B THR* 3.5 5.7 - - - +
31B ILE* 2.7 52.3 + - + +
33B ILE* 4.9 3.1 - - + +
66B LEU* 3.7 29.4 - - + -
75B ASN* 3.3 19.7 - - + +
76B VAL* 4.2 3.1 - - + -
77B VAL* 4.4 0.9 - - - +
126B ILE* 1.3 74.4 - - - +
128B VAL* 1.3 65.0 + - - +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG* 3.4 11.9 - - + +
30B THR* 4.5 13.2 - - + +
71B CYS* 4.7 1.3 - - - -
75B ASN* 3.0 32.2 + - - +
77B VAL* 4.0 16.8 - - + -
126B ILE* 5.4 0.4 - - + -
127B ALA* 1.3 79.7 - - - +
129B GLN* 1.3 73.1 + - - +
132B LEU* 3.8 11.8 - - + +
4C LEU* 3.8 23.3 - - + -
27C VAL* 3.6 37.5 - - + -
32C TYR* 5.5 1.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il